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        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.


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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.11

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the nf-core/quantms analysis pipeline. For information about how to interpret these results, please see the documentation.

        Report generated on 2022-06-08, 15:04 based on data in: /home/chengxin/pmultiqctest/test_iso/results


        pmultiqc

        pmultiqc is an module to show the pipeline performance.

        Experimental Design

        This plot shows the Proteomics Experimental Design

        This plot shows the Proteomics Experimental Design. You can see details about it in https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/classOpenMS_1_1ExperimentalDesign.html

        Showing 2/2 rows and 6/6 columns.
        Spectra FileFraction_GroupFractionLabelSampleMSstats_ConditionMSstats_BioReplicate
        TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML11
        1|2|3|4|5|6
        1|2|3|4|5|6
        SP=Yeast;CT=protein;AC=P00924;QY=10SP=Yeast;CT=protein;AC=P00924;QY=5SP=Yeast;CT=protein;AC=P00924;QY=2.5SP=Yeast;CT=protein;AC=P00924;QY=1SP=Yeast;CT=protein;AC=P00924;QY=2.5SP=Yeast;CT=protein;AC=P00924;QY=10
        1|2|3|4|5|6
        TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_02.mzML21
        1|2|3|4|5|6
        7|8|9|10|11|12
        SP=Yeast;CT=protein;AC=P00924;QY=10SP=Yeast;CT=protein;AC=P00924;QY=5SP=Yeast;CT=protein;AC=P00924;QY=2.5SP=Yeast;CT=protein;AC=P00924;QY=1SP=Yeast;CT=protein;AC=P00924;QY=2.5SP=Yeast;CT=protein;AC=P00924;QY=10
        7|8|9|10|11|12

        HeatMap

        This plot shows the pipeline performance overview

        This plot shows the pipeline performance overview. Some metrics are calculated.

        • Heatmap score[Contaminants]: as fraction of summed intensity with 0 = sample full of contaminants; 1 = no contaminants
        • Heatmap score[Pep Intensity (>23.0)]: Linear scale of the median intensity reaching the threshold, i.e. reaching 2^21 of 2^23 gives score 0.25.
        • Heatmap score[Charge]: Deviation of the charge 2 proportion from a representative Raw file (median). For typtic digests, peptides of charge 2 (one N-terminal and one at tryptic C-terminal R or K residue) should be dominant. Ionization issues (voltage?), in-source fragmentation, missed cleavages and buffer irregularities can cause a shift (see Bittremieux 2017, DOI: 10.1002/mas.21544 ).
        • Heatmap score [MC]: the fraction (0% - 100%) of fully cleaved peptides per Raw file
        • Heatmap score [MC Var]: each Raw file is scored for its deviation from the ‘average’ digestion state of the current study.
        • Heatmap score [ID rate over RT]: Judge column occupancy over retention time. Ideally, the LC gradient is chosen such that the number of identifications (here, after FDR filtering) is uniform over time, to ensure consistent instrument duty cycles. Sharp peaks and uneven distribution of identifications over time indicate potential for LC gradient optimization.Scored using ‘Uniform’ scoring function. i.e. constant receives good score, extreme shapes are bad.
        • Heatmap score [MS2 Oversampling]: The percentage of non-oversampled 3D-peaks. An oversampled 3D-peak is defined as a peak whose peptide ion (same sequence and same charge state) was identified by at least two distinct MS2 spectra in the same Raw file. For high complexity samples, oversampling of individual 3D-peaks automatically leads to undersampling or even omission of other 3D-peaks, reducing the number of identified peptides.
        • Heatmap score [Pep Missing]: Linear scale of the fraction of missing peptides.
        loading..

        Summary Table

        This plot shows the quantms pipeline summary statistics

        This plot shows the quantms pipeline summary statistics

        Showing 1/1 rows and 5/5 columns.
        Total MS/MS SpectralTotal MS/MS Spectral IdentifiedIdentified MS/MS Spectral CoverageTotal Peptide IdentifiedTotal Protein IdentifiedTotal Protein Quantified
        12206
        3084
        25.27%
        1183
        488
        488

        Pipeline Result Statistics

        This plot shows the quantms pipeline final result

        This plot shows the quantms pipeline final result. Including Sample Name、Possible Study Variables、identified the number of peptide in the pipeline、 and identified the number of modified peptide in the pipeline, eg. All data in this table are obtained from the out_msstats file. You can also remove the decoy with the remove_decoy parameter.

        Showing 2/2 rows and 7/7 columns.
        Spectra FileSample Nameconditionfractionpeptide_numunique_peptide_nummodified_peptide_numprotein_num
        TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML
        1|2|3|4|5|6
        SP=Yeast;CT=protein;AC=P00924;QY=10SP=Yeast;CT=protein;AC=P00924;QY=5SP=Yeast;CT=protein;AC=P00924;QY=2.5SP=Yeast;CT=protein;AC=P00924;QY=1SP=Yeast;CT=protein;AC=P00924;QY=2.5SP=Yeast;CT=protein;AC=P00924;QY=10
        1
        1214
        1185
        1214
        504
        TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_02.mzML
        7|8|9|10|11|12
        SP=Yeast;CT=protein;AC=P00924;QY=10SP=Yeast;CT=protein;AC=P00924;QY=5SP=Yeast;CT=protein;AC=P00924;QY=2.5SP=Yeast;CT=protein;AC=P00924;QY=1SP=Yeast;CT=protein;AC=P00924;QY=2.5SP=Yeast;CT=protein;AC=P00924;QY=10
        1
        1214
        1185
        1214
        504

        Number of Peptides Per Protein

        This plot shows the number of peptides per proteins in quantms pipeline final result

        This statistic is extracted from the out_msstats file. Proteins supported by more peptide identifications can constitute more confident results.

        loading..

        Spectra Tracking

        This plot shows the quantms pipeline mzML tracking

        This table shows the changes in the number of spectra corresponding to each input file during the pipeline operation. And the number of peptides finally identified is obtained from the PSM table in the mzTab file. You can also remove the decoy with the remove_decoy parameter.:

        • MS1_Num: The number of MS1 spectra extracted from mzMLs
        • MS2_Num: The number of MS2 spectra extracted from mzMLs
        • MSGF: The Number of spectra identified by MSGF search engine
        • Comet: The Number of spectra identified by Comet search engine
        • Final result of spectra: extracted from PSM table in mzTab file
        • Final result of Peptides: extracted from PSM table in mzTab file
        Showing 2/2 rows and 6/6 columns.
        Spectra FileMS1_NumMS2_NumFinal result of spectraCometFinal result of PeptidesMSGF
        TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML
        1431
        6103
        1542
        3309
        1183
        3103
        TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_02.mzML
        1431
        6103
        1542
        3309
        1183
        3103

        Distribution of precursor charges

        This is a bar chart representing the distribution of the precursor ion charges for a given whole experiment.

        This information can be used to identify potential ionization problems including many 1+ charges from an ESI ionization source or an unexpected distribution of charges. MALDI experiments are expected to contain almost exclusively 1+ charged ions. An unexpected charge distribution may furthermore be caused by specific search engine parameter settings such as limiting the search to specific ion charges.

        loading..

        Number of Peaks per MS/MS spectrum

        This chart represents a histogram containing the number of peaks per MS/MS spectrum in a given experiment. This chart assumes centroid data. Too few peaks can identify poor fragmentation or a detector fault, as opposed to a large number of peaks representing very noisy spectra. This chart is extensively dependent on the pre-processing steps performed to the spectra (centroiding, deconvolution, peak picking approach, etc).

        loading..

        Peak Intensity Distribution

        This is a histogram representing the ion intensity vs. the frequency for all MS2 spectra in a whole given experiment. It is possible to filter the information for all, identified and unidentified spectra. This plot can give a general estimation of the noise level of the spectra.

        Generally, one should expect to have a high number of low intensity noise peaks with a low number of high intensity signal peaks. A disproportionate number of high signal peaks may indicate heavy spectrum pre-filtering or potential experimental problems. In the case of data reuse this plot can be useful in identifying the requirement for pre-processing of the spectra prior to any downstream analysis. The quality of the identifications is not linked to this data as most search engines perform internal spectrum pre-processing before matching the spectra. Thus, the spectra reported are not necessarily pre-processed since the search engine may have applied the pre-processing step internally. This pre-processing is not necessarily reported in the experimental metadata.

        loading..

        Oversampling Distribution

        An oversampled 3D-peak is defined as a peak whose peptide ion (same sequence and same charge state) was identified by at least two distinct MS2 spectra in the same Raw file.

        For high complexity samples, oversampling of individual 3D-peaks automatically leads to undersampling or even omission of other 3D-peaks, reducing the number of identified peptides. Oversampling occurs in low-complexity samples or long LC gradients, as well as undersized dynamic exclusion windows for data independent acquisitions.

                    * Heatmap score [EVD: MS2 Oversampling]: The percentage of non-oversampled 3D-peaks.
        
        loading..

        Delta Mass

        This chart represents the distribution of the relative frequency of experimental precursor ion mass (m/z) - theoretical precursor ion mass (m/z).

        Mass deltas close to zero reflect more accurate identifications and also that the reporting of the amino acid modifications and charges have been done accurately. This plot can highlight systematic bias if not centered on zero. Other distributions can reflect modifications not being reported properly. Also it is easy to see the different between the target and the decoys identifications.

        loading..

        Peptides Quantification Table

        This plot shows the quantification information of peptidesin quantms pipeline final result

        The quantification information of peptides is obtained from the MSstats input file. The table shows the quantitative level and distribution of peptides in different study variables, run and peptiforms. The distribution show all the intensity values in a bar plot above and below the average intensity for all the fractions, runs and peptiforms.

        Showing 50/50 rows and 12/12 columns.
        indexProteinNamePeptideSequenceBestSearchScoreAverage IntensitySP=Yeast;CT=protein;AC=P00924;QY=5SP=Yeast;CT=protein;AC=P00924;QY=2.5SP=Yeast;CT=protein;AC=P00924;QY=1SP=Yeast;CT=protein;AC=P00924;QY=10SP=Yeast;CT=protein;AC=P00924;QY=5SP=Yeast;CT=protein;AC=P00924;QY=2.5SP=Yeast;CT=protein;AC=P00924;QY=1SP=Yeast;CT=protein;AC=P00924;QY=10
        1
        ECA3566
        .(TMT6plex)AAAASK(TMT6plex)
        0.995
        3359784.750
        0.000
        6717307.000
        0.000
        6721832.000
        2
        ECA4049
        .(TMT6plex)AADDAK(TMT6plex)
        0.995
        12850179.625
        0.000
        25731231.500
        0.000
        25669487.000
        3
        ECA3787
        .(TMT6plex)AADLGLETVLVER
        0.995
        3197147.875
        0.000
        6540220.000
        0.000
        6248371.500
        4
        ECA3889
        .(TMT6plex)AAFAFPAPIAPVEDDVAALELFHGPTLAFK(TMT6plex)
        0.995
        9351.092
        0.000
        20684.290
        0.000
        16720.080
        5
        ECA1264
        .(TMT6plex)AAGSLVK(TMT6plex)
        0.995
        2488834.250
        0.000
        5041052.500
        0.000
        4914284.500
        6
        ECA3236
        .(TMT6plex)AAIADYK(TMT6plex)
        0.995
        1295443.500
        0.000
        2567394.000
        0.000
        2614380.000
        7
        ECA1363
        .(TMT6plex)AAIDPLVGPQPYQGR
        0.995
        126093.813
        0.000
        263285.100
        0.000
        241090.150
        8
        ECA4012
        .(TMT6plex)AAIEAAGGK(TMT6plex)
        0.995
        3349177.625
        0.000
        6662684.000
        0.000
        6734026.500
        9
        ECA2190
        .(TMT6plex)AAIEALEQELQVLLLPK(TMT6plex)
        0.995
        11287.716
        0.000
        20225.440
        0.000
        24925.425
        10
        ECA2478
        .(TMT6plex)AAIEGNIPLIPGISTVSELMLGMDYGLR
        0.995
        3884.428
        0.000
        7791.411
        0.000
        7746.299
        11
        ECA2439
        .(TMT6plex)AAIEYAITNDR
        0.995
        679139.375
        0.000
        1359073.500
        0.000
        1357484.000
        12
        ECA3810
        .(TMT6plex)AALEGADMVFIAAGMGGGTGTGAAPVVAEVAK(TMT6plex)
        0.995
        18669.714
        0.000
        31066.075
        0.000
        43612.780
        13
        ECA4007
        .(TMT6plex)AALELAEQR
        0.995
        4227275.000
        0.000
        8706988.500
        0.000
        8202111.500
        14
        ECA0238
        .(TMT6plex)AALESTLAAITESLK(TMT6plex)
        0.995
        12478182.079
        0.000
        25028583.380
        0.000
        24884144.935
        15
        ECA1751
        .(TMT6plex)AALIDC(Methylthio)LAPDR
        0.995
        870156.500
        0.000
        1762596.000
        0.000
        1718030.000
        16
        ECA3362
        .(TMT6plex)AAMSDVLK(TMT6plex)
        0.995
        2233144.375
        0.000
        4390581.500
        0.000
        4541996.000
        17
        ECA2273
        .(TMT6plex)AANVIGIGINGVDAVSELSK(TMT6plex)
        0.995
        59256.270
        0.000
        113672.925
        0.000
        123352.155
        18
        ECA2496
        .(TMT6plex)AAQDGK(TMT6plex)
        0.995
        635712.500
        0.000
        1277707.000
        0.000
        1265143.000
        19
        ECA2494
        .(TMT6plex)AAQDSK(TMT6plex)
        0.994
        922789.500
        0.000
        1842127.000
        0.000
        1849031.000
        20
        ECA4513
        .(TMT6plex)AASFFGSVGGNIVAQVTGMGDNPSVSELIGPVK(TMT6plex)
        0.995
        3182.475
        0.000
        6734.403
        0.000
        5995.497
        21
        ECA1147
        .(TMT6plex)AATAEDR
        0.995
        35514.310
        0.000
        73382.305
        0.000
        68674.935
        22
        ECA4513
        .(TMT6plex)AATDNGGSLIK(TMT6plex)
        0.995
        1201293.375
        0.000
        2443862.500
        0.000
        2361311.000
        23
        ECA4006
        .(TMT6plex)AATILAEQLEAFVDLR
        0.995
        175692.833
        0.000
        377496.175
        0.000
        325275.155
        24
        ECA0402
        .(TMT6plex)AAVLAK(TMT6plex)
        0.995
        1741573.125
        0.000
        3621197.000
        0.000
        3345095.500
        25
        ECA0819
        .(TMT6plex)AAVLESAGINDQSLIEWIK(TMT6plex)
        0.995
        20270.785
        0.000
        41771.150
        0.000
        39311.990
        26
        ECA0871
        .(TMT6plex)AAYAIEDNGAR
        0.995
        141864.338
        0.000
        289388.400
        0.000
        278068.950
        27
        ECA0621
        .(TMT6plex)AC(Methylthio)DEVLNNGK(TMT6plex)
        0.995
        481846.763
        0.000
        979574.100
        0.000
        947812.950
        28
        ECA0685
        .(TMT6plex)AC(Methylthio)IGIITNPVNTTVAIAAEVLK(TMT6plex)
        0.995
        197533.701
        0.000
        400457.700
        0.000
        389677.105
        29
        ECA2831
        .(TMT6plex)ADFNLAGLLPEAVETIEEQAER
        0.995
        208521.639
        0.000
        414458.884
        0.000
        419627.672
        30
        ECA1444
        .(TMT6plex)ADIANLLLAPYFK(TMT6plex)
        0.995
        844188.525
        0.000
        1712798.100
        0.000
        1663956.000
        31
        ECA4267
        .(TMT6plex)ADISADEVAGIGITNQR
        0.995
        105652.650
        0.000
        222087.500
        0.000
        200523.100
        32
        ECA4281;ECA4290
        .(TMT6plex)ADLLPDSDQQALIAVLDSFVK(TMT6plex)
        0.995
        15174.799
        0.000
        30244.504
        0.000
        30454.693
        33
        ECA4516
        .(TMT6plex)AEAEAER
        0.995
        174559.737
        0.000
        351378.100
        0.000
        346860.850
        34
        ECA1867
        .(TMT6plex)AEAGDVANAIIDGTDAVMLSGESAK(TMT6plex)
        0.995
        28635.830
        0.000
        61717.080
        0.000
        52826.240
        35
        ECA4221
        .(TMT6plex)AEAIAEK(TMT6plex)
        0.995
        195603.712
        0.000
        401251.850
        0.000
        381163.000
        36
        ECA2481
        .(TMT6plex)AEAVC(Methylthio)SDAAMDDIILASDVVMVAR
        0.995
        11115.416
        0.000
        25701.355
        0.000
        18760.310
        37
        ECA3810
        .(TMT6plex)AEEAAEMAISSPLLEDIDLSGAR
        0.995
        38864.069
        0.000
        80560.190
        0.000
        74896.085
        38
        ECA0894
        .(TMT6plex)AEEIVASDPSR
        0.995
        1385620.500
        0.000
        2856407.000
        0.000
        2686075.000
        39
        ECA0224
        .(TMT6plex)AEIIEEAETEVAEIQEQFQSGLVTAGER
        0.995
        776.488
        0.000
        3105.951
        0.000
        0.000
        40
        ECA1032
        .(TMT6plex)AEITASLVK(TMT6plex)
        0.995
        3246568.625
        0.000
        6663734.000
        0.000
        6322540.500
        41
        ECA0185
        .(TMT6plex)AELDGK(TMT6plex)
        0.994
        587186.000
        0.000
        1165542.000
        0.000
        1183202.000
        42
        ECA0385
        .(TMT6plex)AELIDAQVEQLLALAER
        0.995
        299102.843
        0.000
        617069.715
        0.000
        579341.655
        43
        ECA0842
        .(TMT6plex)AEMDIEK(TMT6plex)
        0.995
        313081.750
        0.000
        609719.950
        0.000
        642607.050
        44
        ECA2460
        .(TMT6plex)AEQQAK(TMT6plex)
        0.995
        590761.750
        0.000
        1179675.000
        0.000
        1183372.000
        45
        ECA0639
        .(TMT6plex)AESALK(TMT6plex)
        0.995
        87859.425
        0.000
        179030.700
        0.000
        172407.000
        46
        ECA1456
        .(TMT6plex)AEVEQAIASAAAAFPAWSK(TMT6plex)
        0.995
        85080.363
        0.000
        180347.850
        0.000
        159973.600
        47
        ECA2481
        .(TMT6plex)AEVMDVANAVLDGTDAVMLSAETAAGQYPAETVAAMAK(TMT6plex)
        0.995
        11422.074
        0.000
        18005.430
        0.000
        27682.865
        48
        ECA0690
        .(TMT6plex)AEVVAHGR
        0.995
        348676.375
        0.000
        670733.650
        0.000
        723971.850
        49
        ECA4426
        .(TMT6plex)AEWDNVTVR
        0.995
        978563.500
        0.000
        2008726.500
        0.000
        1905527.500
        50
        ECA1853
        .(TMT6plex)AFDFAC(Methylthio)LPNDGVGLAR
        0.995
        197836.884
        0.000
        414278.105
        0.000
        377069.430
        First Page Previous PageNext Page Last PagePage/Total Pages

        Protein Quantification Table

        This plot shows the quantification information of proteinsin quantms pipeline final result

        The quantification information of proteins is obtained from the msstats input file. The table shows the quantitative level and distribution of proteins in different study variables and run.

        Showing 50/50 rows and 10/10 columns.
        ProteinNamePeptides_NumberAverage IntensitySP=Yeast;CT=protein;AC=P00924;QY=5SP=Yeast;CT=protein;AC=P00924;QY=2.5SP=Yeast;CT=protein;AC=P00924;QY=1SP=Yeast;CT=protein;AC=P00924;QY=10SP=Yeast;CT=protein;AC=P00924;QY=5SP=Yeast;CT=protein;AC=P00924;QY=2.5SP=Yeast;CT=protein;AC=P00924;QY=1SP=Yeast;CT=protein;AC=P00924;QY=10
        ECA0003
        2
        352951.125
        0.000
        714566.100
        0.000
        697238.400
        ECA0013
        3
        1234851.788
        0.000
        2443909.325
        0.000
        2495497.825
        ECA0029
        5
        1630532.158
        0.000
        3408940.583
        0.000
        3113188.050
        ECA0030
        1
        115755.050
        0.000
        236707.850
        0.000
        226312.350
        ECA0050
        1
        10787.644
        0.000
        20387.920
        0.000
        22762.656
        ECA0055
        5
        508904.369
        0.000
        1061315.205
        0.000
        974302.270
        ECA0077
        1
        4713987.500
        0.000
        9320658.000
        0.000
        9535292.000
        ECA0078
        1
        12669.655
        0.000
        25573.780
        0.000
        25104.840
        ECA0085
        1
        1902.056
        0.000
        3938.225
        0.000
        3670.000
        ECA0091
        1
        521133.875
        0.000
        1028170.000
        0.000
        1056365.500
        ECA0092
        5
        7852577.032
        0.000
        15875112.340
        0.000
        15535195.790
        ECA0094
        1
        31349.079
        0.000
        61132.565
        0.000
        64263.750
        ECA0098
        1
        19469.809
        0.000
        40953.430
        0.000
        36925.805
        ECA0102
        1
        11944.612
        0.000
        26302.090
        0.000
        21476.360
        ECA0104
        4
        973002.938
        0.000
        2018158.800
        0.000
        1873852.950
        ECA0125
        1
        45697.932
        0.000
        97321.375
        0.000
        85470.355
        ECA0130
        2
        1171119.839
        0.000
        2412881.813
        0.000
        2271597.542
        ECA0146
        1
        469671.337
        0.000
        941318.900
        0.000
        937366.450
        ECA0172
        3
        4352065.246
        0.000
        8865825.600
        0.000
        8542435.382
        ECA0185
        1
        587186.000
        0.000
        1165542.000
        0.000
        1183202.000
        ECA0193
        1
        108392.650
        0.000
        231775.450
        0.000
        201795.150
        ECA0208
        1
        490777.000
        0.000
        1054568.600
        0.000
        908539.400
        ECA0216;ECA4035
        15
        34375575.230
        0.000
        71473087.230
        0.000
        66029213.690
        ECA0219
        2
        8897154.250
        0.000
        18530314.000
        0.000
        17058303.000
        ECA0220
        3
        8030299.200
        0.000
        16250598.200
        0.000
        15870598.600
        ECA0221
        4
        9340782.875
        0.000
        19299904.000
        0.000
        18063227.500
        ECA0222
        5
        5194441.172
        0.000
        10585184.055
        0.000
        10192580.631
        ECA0223
        10
        1242137.674
        0.000
        2580898.725
        0.000
        2387651.970
        ECA0224
        9
        1116532.912
        0.000
        2303681.076
        0.000
        2162450.570
        ECA0238
        2
        12686180.141
        0.000
        25462242.580
        0.000
        25282477.985
        ECA0247
        2
        1006856.650
        0.000
        2113405.440
        0.000
        1914021.160
        ECA0255
        1
        26513.070
        0.000
        50843.680
        0.000
        55208.600
        ECA0260
        1
        34649.475
        0.000
        65471.470
        0.000
        73126.430
        ECA0261
        1
        37518.295
        0.000
        78791.075
        0.000
        71282.105
        ECA0264
        1
        1046829.625
        0.000
        2087504.000
        0.000
        2099814.500
        ECA0265
        2
        118677.345
        0.000
        252766.250
        0.000
        221943.130
        ECA0267
        1
        32339.714
        0.000
        69068.405
        0.000
        60290.450
        ECA0273
        1
        9859.484
        0.000
        19007.790
        0.000
        20430.145
        ECA0281
        1
        4688.390
        0.000
        9005.025
        0.000
        9748.533
        ECA0282
        1
        12151.046
        0.000
        27335.559
        0.000
        21268.625
        ECA0287
        1
        419745.350
        0.000
        905889.800
        0.000
        773091.600
        ECA0293
        1
        39778.551
        0.000
        88715.425
        0.000
        70398.780
        ECA0301
        1
        613737.375
        0.000
        1271307.000
        0.000
        1183642.500
        ECA0303
        3
        421311.037
        0.000
        874571.310
        0.000
        810672.838
        ECA0306
        2
        2386772.550
        0.000
        4951834.950
        0.000
        4595255.250
        ECA0308
        3
        155125.652
        0.000
        316225.020
        0.000
        304277.590
        ECA0310
        5
        3008517.324
        0.000
        6163302.325
        0.000
        5870766.970
        ECA0316
        1
        6044.405
        0.000
        11756.815
        0.000
        12420.805
        ECA0333
        1
        16970.860
        0.000
        34893.980
        0.000
        32989.460
        ECA0372
        2
        1004841.682
        0.000
        2034471.535
        0.000
        1984895.192
        First Page Previous PageNext Page Last PagePage/Total Pages

        nf-core/quantms Software Versions

        are collected at run time from the software output.

        Process Name Software Version
        CONSENSUSID ConsensusID 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        CUSTOM_DUMPSOFTWAREVERSIONS python 3.9.5
        yaml 5.4.1
        DECOYDATABASE DecoyDatabase 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        EXTRACTPSMFEATURES PSMFeatureExtractor 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        FDRCONSENSUSID FalseDiscoveryRate 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        FILEMERGE FileMerger 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        IDCONFLICTRESOLVER IDConflictResolver 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        IDFILTER IDFilter 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        IDMAPPER IDMapper 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        ISOBARICANALYZER IsobaricAnalyzer 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        MSSTATSCONVERTER MSstatsConverter 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        MSSTATSTMT bioconductor-msstatstmt 2.2.0
        r-base 4.1.1
        MZMLINDEXING FileConverter 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        PERCOLATOR PercolatorAdapter 2.8.0-pre-exported-20220227 Feb 27 2022, 20:31:47
        percolator 3.05.0, Build Date Aug 31 2020 19:03:04
        PROTEININFERENCER ProteinInference 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        PROTEINQUANTIFIER ProteinQuantifier 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        SAMPLESHEET_CHECK sdrf-pipelines 0.0.21
        SDRFPARSING sdrf-pipelines 0.0.21
        SEARCHENGINECOMET Comet 2019.01 rev. 5
        CometAdapter 2.8.0-pre-exported-20220227 Feb 27 2022, 20:31:47
        SEARCHENGINEMSGF MSGFPlusAdapter 2.8.0-pre-exported-20220227 Feb 27 2022, 20:31:47
        msgf_plus MS-GF+ Release (v2021.03.22) (22 March 2021)
        Workflow Nextflow 21.10.6
        nf-core/quantms 1.1dev

        nf-core/quantms Workflow Summary

        - this information is collected when the pipeline is started.

        Core Nextflow options

        runName
        lethal_rosalind
        containerEngine
        docker
        launchDir
        /home/chengxin/newPR/quantms
        workDir
        /home/chengxin/newPR/quantms/work
        projectDir
        /home/chengxin/newPR/quantms
        userName
        chengxin
        profile
        test_tmt,docker
        configFiles
        /home/chengxin/newPR/quantms/nextflow.config

        Input/output options

        input
        /home/chengxin/tmt_testdata/PXD000001.sdrf.tsv
        outdir
        ./results_iso
        root_folder
        /home/chengxin/tmt_testdata/

        Protein database

        database
        /home/chengxin/tmt_testdata/erwinia_carotovora.fasta
        add_decoys
        true
        decoy_string
        rev

        Database search

        search_engines
        msgf,comet
        instrument
        N/A
        protocol
        TMT

        Modification localization

        luciphor_debug
        N/A

        PSM re-scoring (general)

        run_fdr_cutoff
        0.10

        PSM re-scoring (Percolator)

        description_correct_features
        N/A

        Consensus ID

        consensusid_considered_top_hits
        N/A
        min_consensus_support
        N/A

        Isobaric analyzer

        select_activation
        HCD

        Protein inference

        psm_level_fdr_cutoff
        1.0

        Protein Quantification (DDA)

        ratios
        N/A
        normalize
        N/A
        fix_peptides
        N/A

        DIA-NN

        acquisition_method
        N/A
        mass_acc_ms2
        13
        mass_acc_ms1
        7
        scan_window
        8

        Statistical post-processing

        contrasts
        pairwise

        Quality control

        enable_pmultiqc
        true

        Institutional config options

        config_profile_name
        Full test profile DDA ISO
        config_profile_description
        Full test dataset in isotopic labelling mode to check pipeline function and sanity of results

        Max job request options

        max_cpus
        2
        max_memory
        6 GB
        max_time
        2d

        Generic options

        hostnames
        N/A